6VUI

Metabolite-bound PreQ1 riboswitch with Mn2+

6VUI の概要

• エントリーDOI: 10.2210/pdb6vui/pdb
• 関連するPDBエントリー: 3Q50 3Q51
• 分子名称: PREQ1 RIBOSWITCH, 7-DEAZA-7-AMINOMETHYL-GUANINE, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: preq1, preq0, queuosine, ribosomal binding site, aptamer, metabolite, pseudoknot, h-type, riboswitch, rna
• 由来する生物種: Caldanaerobacter subterraneus subsp. tengcongensis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 11108.22

構造登録者

Jenkins, J.L.,Wedekind, J.E. (登録日: 2020-02-15, 公開日: 2020-06-24, 最終更新日: 2023-10-11)

主引用文献

Schroeder, G.M.,Dutta, D.,Cavender, C.E.,Jenkins, J.L.,Pritchett, E.M.,Baker, C.D.,Ashton, J.M.,Mathews, D.H.,Wedekind, J.E.
Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.
Nucleic Acids Res., 48:8146-8164, 2020

PubMed Abstract: Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

PubMed: 32597951
DOI: 10.1093/nar/gkaa546

実験手法

X-RAY DIFFRACTION (2.681 Å)